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Department of Microbiology

Microbiology ServicesUser Handbook

Department of MicrobiologyGreat Western HospitalMarlborough RoadSwindonWiltshireSN3 6BB

DCN: MIC-P-006-10.0 November 2012 of 18


Contents

Document Control..............................................................................................................................2

General Information...........................................................................................................................3

Contact Details...................................................................................................................................3

Service Availability..............................................................................................................................3

Laboratory Location............................................................................................................................4

Results................................................................................................................................................5

Clinical Advice.....................................................................................................................................5

Requesting Tests.................................................................................................................................5

Specimen Transport............................................................................................................................5

Specimen Containers..............................................................................................................................5Request Forms.......................................................................................................................................5Health & Safety......................................................................................................................................6

Quality Management..........................................................................................................................7

External Quality Assurance.....................................................................................................................7Turnaround Times..................................................................................................................................7

Reference Laboratories.......................................................................................................................7

External Service providers...................................................................................................................8

Bacteriology Tests...............................................................................................................................9

Virology Tests...................................................................................................................................14

DOCUMENT CONTROL

This handbook is subject to the document control procedures used in the Pathology Directorate. As this version is controlled electronically, any printed hardcopy copy or locally-saved electronic copy will no longer be subject to the control procedures. Please ensure that any reference is made to the current active version of this document.



GENERAL INFORMATION

The Clinical Microbiology Service is provided by the laboratories at the Great Western Hospital, Swindon. We provide an analytical and interpretative service on a wide-range of clinical specimens, processing over 260,000 requests each year. The efficiency of the service we provide is reliant on the cooperation of our users with the necessary policies relating to safety, specimen transport and specimen identification.

We hope that this handbook contains all the information you require to use our service. However, please feel free to contact us to discuss any problems or issues you may have. Any comments or suggestions about the User Handbook should be addressed to the Laboratory Manager, by email to [email protected].

We aim to be a model of excellence in the delivery of a clinical pathology service. In order to achieve this, we are committed to the following:

Service user involvement Good professional practice & evidence-based practice Efficient utilisation of our resources Valuing and developing our staff in order to realise their full potential Commitment to the health, safety and welfare of our patients, staff and visitors Keeping a safe environment in compliance with current environmental legislation Working as teams and partnerships Continuous improvement

CONTACT DETAILS

Consultant Microbiologist Dr Melanie Wilson (01793) 604801Consultant Microbiologist Dr Susan Dawson (01793) 604802Deputy General Manager David Newell (01793) 605013Laboratory Manager Penny Latham (01793) 604804Section Manager (Virology) Helen Jones (01793) 604799

SERVICE AVAILABILITY

The laboratories are open for receipt of specimens from 0845 to 1700 between Monday and Friday, 0800 to 1300 on Saturday mornings and 0845 to 1230 on Sunday mornings and Bank Holidays. There is a refrigerator in the Pathology Reception (and an incubator for blood culture bottles) for specimens that arrive outside the normal opening hours. Certain specimens may be sent direct to the laboratories using the pneumatic chute system (Pathology Address: 104).

The on-call service is available outside normal hours. The use of the service should be restricted to those samples where it is essential to have a result before the next routine session. In general, samples normally accepted for the on-call service would include CSF, joint fluids, pleural fluids, ascitic fluids, pus


mailto:[email protected]


and urine. To discuss an urgent specimen with the duty Biomedical Scientist, please contact switchboard at GWH (01793 604020).

LABORATORY LOCATION

The Department is part of the Directorate of Pathology, within the Great Western Hospitals NHS Foundation Trust. The department is sited on the fourth floor of the main hospital building (see diagram). The postal address is as follows:

Department of MicrobiologyGreat Western Hospitals NHS Foundation TrustThe Great Western HospitalMarlborough RoadSwindonWiltshireSN3 6BB


Department of Microbiology (67)

Directorate of Pathology (69)


RESULTS

Please note that we need to establish the caller’s identity before giving results over the telephone. We are unable to give results directly to patients or their relatives.

Authorised results are available on the Medway system and the Ward Enquiry system. Results may also be obtained by telephoning extension 4293 (direct dial 01793 604293).

In general, results are not available until they have been authorised. In exceptional circumstances, preliminary results may be available direct from the relevant laboratory. However, please bear in mind that this may delay the testing of other samples.

Microbiology Extension 4798Virology Extension 4799

CLINICAL ADVICE

For clinical advice on the interpretation of results, please contact the duty Consultant. During the out-of-hours period, the duty Consultant can be contacted via GWH switchboard.

Consultant Microbiologist Dr Melanie Wilson (01793) 604798Consultant Microbiologist Dr Susan Dawson (01793) 604798

REQUESTING TESTS

A list of tests provided by the Microbiology laboratory is provided in this document. All tests should be requested at the time of submitting the specimen to the laboratory. However, amendments to requests, or the need for additional tests, can still be discussed with the laboratory after processing has started. In general, additional tests must be requested within 48 hours of sample receipt within the laboratory. In some cases, additional tests may not be possible and a fresh specimen will be required. Further advice can be obtained from the laboratory.

SPECIMEN TRANSPORT

Refer to Specimen Transportation Policy available on the Trust intranet.

Specimen ContainersAll patient specimen containers must be clearly labelled with the patient’s name, date of birth, the date of collection and the type of specimen. The hospital number should be included where possible.

Request FormsAll samples must be accompanied by a properly completed request form, giving relevant clinical information, including antibiotics (used or proposed), patient location and detailing the investigation



required. Please note that inadequately labelled specimens and those without adequately completed request forms may not be processed.

The laboratory assumes that patient consent has been obtained for the investigations requested. All requests for HIV investigations must include the Doctor’s signature on the request form.

Health & SafetyAll specimens should be regarded as potentially infectious.

Certain specimens from patients who are known or suspected to have the following diseases/conditions constitute a potential higher risk of infection to persons handling the specimens: Typhoid/paratyphoid fever (faecal specimens only) Dysentery (faecal specimens only) Tuberculosis (specimens from sites where tuberculosis infection is likely) Anthrax Brucellosis Transmissible Spongiform Encephalopathy (including CJD) Viral haemorrhagic fever Pandemic Flu

To minimise the risks “Danger of Infection” labels should be attached to the specimen container and request form for all qualifying specimens (available from Phlebotomy Dept, GWH) and the nature of the risk specified on the request form. This is a necessary procedure to protect persons handling the specimens (nursing, portering, transport, reception and laboratory staff). The labels must be used in accordance with the Specimen Transportation Policy available on the Trust intranet.

Samples thought to constitute a risk to laboratory staff because of inadequate packaging or warning may be rejected.

The Consultant Microbiologist must be contacted BEFORE collecting specimens from a patient suspected of having a viral haemorrhagic fever, human avian influenza, SARS or CJD. These organisms require special transport arrangements and specialist laboratories designed for containment during manipulation of specimens and cultures.

These lists are not exhaustive and rarely other biological agents that can cause severe human disease, and present a serious hazard to employees, may be present in specimens. If there is any suspicion of a high risk atypical organism advice on specimen collection and transport should be sought from the Consultant Microbiologist.



QUALITY MANAGEMENT

The Pathology Service is committed to maintaining accreditation for its quality management system. Accreditation is undertaken by Clinical Pathology Accreditation (UK) Ltd, an independent external organisation. Details of our accreditation, together with performance data, are available from the Laboratory Manager.

In order to help us improve our service, we may ask you to complete a questionnaire. We greatly value the information obtained from these surveys, and we would like to thank you in anticipation of your assistance in completing the questionnaires.

As part of our quality management system, we routinely monitor certain performance indicators. These include External Quality Assurance (EQA) scores and Turnaround Times (TAT).

External Quality AssuranceDuring 2011, our total EQA score was 98.6% (820 points out of a possible 834). The EQA scheme involves a series of simulated specimens being sent to our laboratory for testing. Our results are then scored against the intended results and compared to a national average. Each occasion in which we fail to report the intended result is investigated thoroughly within our quality improvement system.

Turnaround TimesWe monitor the turnaround times for certain key tests every month. The time taken from receipt of specimen to the reporting of the result is analysed for a range of twelve key tests. Details of the target turnaround times for all tests are given in the test section later in this document. During 2011, our total TAT score for the twelve key tests was 98.1%. This meant that we met our target in 98.1% of cases. The total number of tests checked during this period was 239 510. Further details on our TAT performance can be obtained from the Laboratory Manager.

REFERENCE LABORATORIES

As part of the testing process, it may be necessary to refer some, or all, of the specimen to an external reference laboratory. We only use laboratories which have an accredited quality management system. The name of the reference laboratory used will be indicated on the test report. The reference laboratories currently used are:

Anaerobe Reference Laboratory, Cardiff Antimicrobial Reference Unit, Bristol Cryptosporidium Reference Unit, Swansea Health Protection Agency, Birmingham Health Protection Agency, London Health Protection Agency, Bristol Health Protection Agency, Manchester Health Protection Agency, Porton Down Health Protection Agency, Southampton



Immunology Department, Oxford Immunology Department, Bristol Insect Research & Development, Cambridge Lab 21 Clinical Laboratory, Cambridge Leptospira Reference Unit, Hereford Microbiology Department, Epsom Microbiology Department, Leeds Microbiology Department, Exeter Toxoplasma Reference Unit, Swansea Veterinary Laboratory Agency, Surrey

EXTERNAL SERVICE PROVIDERS

Specimens for Mycology and Mycobacterium investigation are referred to an external service provider, Southampton University Hospitals NHS Trust (SUHT), for processing.



BACTERIOLOGY TESTS

Investigation Test Sample(Volume) Container TAT Limitations Out-of-Hours

Antibiotic Levels Antibiotic Assay Clotted blood(2-6mls)

Vacutainer(red-top) 3 days

Requests must be discussed with the

Consultant Microbiologist

no

Ascitic Fluid Culture Cell count, Gram stain & Culture

Ascitic fluid(<20mls)

Universal(white top)

4 days, plus 2 days for

enrichment culture

cell counts performed on SBP patients only

yes, by arrangement

Blood Cultures (Adults)

Gram stain & Culture

Blood(5-10mls)

Adult blood culture set

1-5 days, depending on

positivity

samples should be collected before

antibiotic treatment

bottles should be sent to the

incubator located in Pathology

reception

Blood Cultures (Children)

Gram stain & Culture

Blood(<4mls)

Paediatric blood culture bottle

1-5 days, depending on

positivity

samples should be collected before

antibiotic treatment

bottles should be sent to the

incubator located in Pathology

reception

C. difficile Toxin Toxin Detection Faeces(<20mls)

Universal with spoon (blue top) 1 day

not performed on formed stools; not

performed if a positive result within previous

28 days

no

Corneal Scrape Culture

Gram stain & Culture Corneal scrape Direct inoculation

onto plates and slide

2 hrs for microscopy2-5 days for

culture

requires good amount of cellular material

yes, by arrangement

CSF Culture Cell count, Gram stain & Culture

CSF(1-2mls)

3 sterile universal containers (white

top), labelled 1,2,3

2 hrs for microscopy2 days for

culture

cell counts cannot be performed on clotted

samples

yes, by arrangement

Ear Swab Culture Culture Ear swab Transport swab(blue top) 4 days none no

Eye Swab Culture Culture Eye swab Transport swab(blue top) 4 days none no




Faeces Culture Microscopy & Culture

Faeces(<20mls)

Universal with spoon (blue top) 4 days clinical details are

essential for processing no

Fungal Culture Microscopy & Culture Skin, hair, nails fungal culture kit /

universal (white top)

1 week for microscopy4 weeks for

culture

none no

Gonococcal Culture Culture Urethral swab Transport swab(orange top) 3 days

transport delay may reduce sensitivity of

testno

Gonococcal Culture Culture Endocervical swab Transport swab(blue top) 3 days

transport delay may reduce sensitivity of

testno

Gynaecological Culture

Microscopy & Culture Endocervical swab Transport swab

(blue top) 4 days clinical details are essential for processing no

Gynaecological Culture

Microscopy & Culture Vaginal swab Transport swab

(blue top) 4 days

clinical details are essential for processing

please send endocervical swab if gonococcal culture is

required

no

IV Cannulae Culture Culture End of cannula tip(2-5cm length)

Universal(white top) 4 days none no

Joint Fluid Culture Gram stain, Crystals & Culture

Joint fluid(<20mls)



enrichment culture

none yes, by arrangement

Lavage Culture Gram stain & Culture

Broncho-alveolar lavage

(<20mls)

Universal(white top) 4 days none no




Leg Ulcer Swab Culture Culture Leg ulcer swab Transport swab

(blue top) 4 days

routine swabbing is unnecessary unless

there is indication of infection

no

Mouth Swab Culture Culture Mouth swab Transport swab(blue top) 4 days Culture directed to

Candida sp. no

MRSA Culture Culture for MRSA only Swab / urine

Transport swab (blue top) / universal

container3 days Culture directed to

MRSA only No

MRSA PCR Rapid test for MRSA Swab Transport swab (red

top) 2-4 hours

Limited to Aldbourne patients and patients

who have missed conventional tetsing

No

Neonatal Screen Culture Culture Swabs & gastric

aspirate

Transport swab (blue top) / universal

container4 days swabs from throat,

umbilicus and ear no

Nose Swab Culture Culture forStaph. aureus only Nose swab Transport swab

(blue top) 4 days

pernasal swabs are required for the

isolation of Pertussis sp.

no

Parasitology Microscopy for Schistosomiasis

Urine(<20mls)

Universal(white top) 2 days

Collection of urine between 10am and

2pmno

Parasitology Microscopy Faeces(<20mls)

Universal with spoon (blue top) 2 days none no

Parasitology(Pinworm) Microscopy Sellotape slide

Collection kits available from

laboratory2 days none no




PD Fluid Culture Cell count, Gram stain & Culture

Peritoneal dialysis fluid

(<20mls)



enrichment culture

differential cell counts performed on raised

WBC counts

yes, by arrangement

Pertussis Culture Culture Pernasal swab

Pernasal swab (orange top)

obtained from laboratory

7 days none no

Pleural Fluid Culture Gram stain & Culture

Pleural fluid(<20mls)



enrichment culture


Pus Culture Gram stain & Culture

Pus(<20mls)



enrichment culture


Rotavirus Detection Antigen Detection Faeces(<20mls)

Universal with spoon (blue top) 1 day limited to children

<4years no

Skin Swab Culture Culture Skin swab Transport swab(blue top) 4 days none no

Sputum Culture Gram stain & Culture

Sputum(<20mls)


samples should be collected early morning

or after physiono

TB Culture Culture Early Morning Urine(3x250mls)

250ml bottles obtained from

laboratory6 weeks

no microscopy performed on urine TB

samplesno

TB Culture Microscopy & Culture

Sputum / BAL(<20mls)


2 days for microscopy; 6

weeks for culture

none no




TB Culture Microscopy & Culture Tissue Universal

(white top)

2 days for microscopy; 6

weeks for culture

none no

Teicoplanin Levels Antibiotic Assay Clotted blood(2-6mls)


Requests must be discussed with the

Consultant Microbiologist

no

Throat Swab Culture Culture Throat swab Transport swab(blue top) 4 days Isolation of Neisseria

sp only on request no

Tissue Culture Gram stain & Culture Tissue Universal

(white top)


enrichment culture


Urine Culture Microscopy & Culture

Urine(<20mls)

Universal with boric acid (red top) 3 days none yes, by

arrangement

Urine Legionella Test Antigen Detection Urine(5-20mls)

Universal(white top) <1 day

please contact lab if urgent processing

required

Saturday and Sunday morning, by arrangement

only

Urine Pneumococcal Test Antigen Detection Urine

(5-20mls)Universal

(white top) <1 dayplease contact lab if urgent processing

required


only

Wound Swab Culture Culture Wound swab Transport swab(blue top) 4 days pus sample should be

sent, if available no



VIROLOGY TESTS

Investigation Test Sample Container TAT Limitations Out-of-Hours

Antenatal Serology Antibody Detection

Clotted blood(2-6mls)


requests for HIV test must be clearly

indicated and signedno

ASO Titres Antibody Detection




no

Atypical Pneumonia Antigen DetectionBroncho-alveolar

lavage(<20mls)

Universal(white top) 1 day

please contact lab if urgent processing is

required for PCPno

Atypical Serology Antibody Detection



clinical details and date of onset are essential

for processingno

Bone Donor ScreenAntigen & Antibody Detection




no

Cardiac Virus Serology

Antibody Detection




for processingno

Cardiac Virus PCR DNA Detection by PCR

EDTA sample(2-3mls)

Vacutainer(purple-top) 14 days


for processingno

Chickenpox Serology Antibody Detection


Vacutainer(red-top)

1 day (urgent)7 days

(normal)

please contact lab if urgent processing is

requiredno

CMV Serology Antibody Detection




no




CMV PCR DNA Detection by PCR

EDTA sample(2-3mls)



no

Conjunctival Chlamydia Infection

DNA Detection by PCR Conjunctival swab Chlamydia transport

swab 1-2 days none no

EBV Serology Antibody Detection




no

EBV PCR Antigen Detection EDTA sample(2-3mls)



no

Genital Chlamydia Infection

DNA Detection by PCR

Urine(<20mls)


patient should not have urinated for 2

hours prior to specimen collection

no

Genital Chlamydia Infection

DNA Detection by PCR Endocervical swab Chlamydia transport

swab 4 days none no

Helicobacter Serology

Antibody Detection




no

Hepatitis A Serology Antibody Detection



clinical details are essential for

processing, especially onset date

no

Hepatitis B Antibody Antibody Detection



vaccination history required for full

interpretation of resultno




Hepatitis B Core Antibody

Antibody Detection




no

Hepatitis B Surface Antigen

Antibody Detection



requests must be clearly indicated and signed on the request

form

no

Hepatitis B (DNA) Viral Load

DNA Detection by PCR

EDTA sample(2-3mls)



no

Hepatitis C Serology Antibody Detection



requests must be clearly indicated and signed on the request

form

no

Hepatitis C Viral Load / Genotype

RNA Detection by PCR

EDTA sample(2-3mls)



no

HIV Serology Antibody Detection


Vacutainer(red-top) 7days

requests for HIV test must be clearly

indicated and signedno

HIV Viral Load DNA Detection by PCR

EDTA sample(2-3mls)



no

HSV Serology Antibody Detection




no

Leptospira Serology Antibody Detection



clinical details, date of onset and exposure history are essential

for processing

no




Lymes Serology Antibody Detection



clinical details, tick exposure and date of onset are essential for

processing

no

Meningococcal PCR DNA Detection by PCR

EDTA sample(2-3mls)



no

Parasite Serology Antibody Detection



clinical details, date of onset and travel

history are essential for processing

no

Parvovirus Serology Antibody Detection




no

Pneumococcal PCR DNA Detection by PCR

EDTA sample(2-3mls)



no

RSV Detection Antigen DetectionNasopharyngeal

aspirate(5-10mls)

Trap bottle <1day none


only

Rubella Serology Antibody Detection




no

Syphilis Serology Antibody Detection




no

Toxoplasma Serology Antibody Detection




no




Virus Detection DNA Detection by PCR Viral transport swab Transport swab

(green top) 14 daysclinical details are

essential for processing

no


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